DEVONthink Pro
The Pro edition of DEVONthink 4. A database for the pile, with links, rules, and a memory for what belongs together.
The note and the archive in one window. Image from DEVONtechnologies. 
A smart rule that does the filing. Image from DEVONtechnologies.
DEVONthink is a database for the pile, not another folder. PDFs, mail, images, web archives, and markdown live in one place. The same item can sit in more than one group without being copied. Search runs as you type, including partial matches, which is what you actually remember about a paper three years later.
The part that feels like a second reader is the concordance. See Also and Classify look across the database and suggest what a document belongs with. The graph draws those links: tags, mentions, item links, See Also. Smart rules then do the filing. One of DEVONtechnologies’ own examples is a rule that takes an unread news item and asks the chat to summarize it. You write the condition once.
Pro is the middle of three editions in DEVONthink 4, between Standard and Server, and it unlocks a further set of capabilities. Sync is part of the product, so the library is not stuck on one Mac. You can write in it. Markdown sits next to the files it cites, and an item link jumps from the sentence to the source. It is the tool for a research library that still has to be findable after the project that built it is over.
Buy from DEVONtechnologies: devontechnologies.com .